Molecular modeling based approach, synthesis, and cytotoxic activity of novel benzoin derivatives targeting phosphoinostide 3-kinase (PI3Kα)

A pharmacological perspectives of Musa sapientum peels against lung cancer: An in vitro and in silico study

CONTEXT

The essential role of medicinal plants is studied over 5000 years against the life-threatening diseases such as cancer in developing countries. The more cognizance on molecular mechanism will engender trend to use them efficaciously.

AIMS

To analyze the pharmacological activity of banana peel against lung cancer.

SETTINGS AND DESIGN

Banana fruit is a nutritious victuals with proven medicinal properties. The underlying molecular mechanism of phytochemicals present in the banana peel was studied using in vitro and in silico methods to explore an efficacious anticancer drug against lung cancer.

METHODS AND MATERIALS

The petroleum ether extract of Musa sapientum peel is analyzed using gas chromatography-mass spectrometry, in vitro studies using 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl tetrazolium bromide (MTT), 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and lipid peroxidase assay, and the in silico studies by molecular docking.

STATISTICAL ANALYSIS USED

Microsoft Excel 2010 is used to calculate the mean and standard deviation for the ABTS and lipid peroxidation assay.

RESULTS

The antioxidant activity was found to be 20 µg/ml concentration in ABTS assay and 10 µg/ml concentration in lipid peroxidation assay. The in vitro anticancer activity was inspected using A549 cell lines by MTT assay. Tri cyclo [5,1,0,0 (2, 4) oct 5-ene 5 proponoic acid] 3,3,8,8 tetramethyl was selected as best lead against epidermal growth factor receptor of human based on the energy score calculated using the Auto-dock software.

CONCLUSIONS

This study strongly supports that unexploited banana peels could be used to harvest promising lead molecules against non-small cell lung cancer.

New derivatives of sulfonylhydrazone as potential antitumor agents: Design, synthesis and cheminformatics evaluation

Phosphoinositide 3-kinase α (PI3Kα) is a propitious target for designing anticancer drugs. A series of new N'-(diphenylmethylene)benzenesulfonohydrazide was synthesized and characterized using FT-IR, NMR (¹H and ¹³C), HRMS, and elemental analysis. Target compounds exhibited an antiproliferative effect against the human colon carcinoma (HCT-116) cell line. Our cheminformatics analysis indicated that the para-tailored derivatives [p-NO₂ (3) and p-CF₃ (7)] have better ionization potentials based on calculated Moran autocorrelations and ionization potentials. Subsequent in vitro cell proliferation assays validated our cheminformatics results by providing experimental evidence that both derivatives 3 and 7 exhibited improved antiproliferative activities against HCT-116. Hence, our results emphasized the importance of electron-withdrawing groups and hydrogen bond-acceptors in the rational design of small-molecule chemical ligands targeting PI3Kα. These results agreed with the induced-fit docking against PI3Kα, highlighting the role of p-substituted aromatic rings in guiding the ligand-PI3Kα complex formation, by targeting a hydrophobic pocket in the ligand-binding site and forming π-stacking interactions with a nearby tryptophan residue.

Synthesis, biological evaluation (antioxidant, antimicrobial, enzyme inhibition, and cytotoxic) and molecular docking study of hydroxy methoxy benzoin/benzil analogous

In this work, due to the biological activity evaluation, a series of hydroxy methoxy benzoins (1-8), benzils (10-16) and methoxy benzoin/benzil-O-β-d-glucosides (17-28) were synthesized. Antioxidant (FRAP, CUPRAC, DPPH), antimicrobial (16 microorganisms, and two yeast), enzyme inhibition (α-amylase, α-glucosidase, AChE, BChE, and tyrosinase) of all synthesized benzoin/benzil analogs were investigated. Benzoins (1-8) showed the most effective antioxidant properties compared to all three methods. Compound 28 against α-amylase, compound 9 against α-glucosidase, compound 11 against AChE, compound 2 against BChE, and compound 13 against tyrosinase showed the best activities with the better or similar IC₅₀ values as used standards. Hydroxy methoxy benzoin compounds (1-8) among all four groups were seen as the most effective against the tested microorganism. Molecular docking analysis showed that all tested compounds 1-28 (0.01-2.22 µM) had the best binding affinity against AChE enzyme. Cytotoxic effects of the many of compounds (1-16, 21, and 24) also investigated and it was found that they caused different effects in different cells. The LDH tests of compounds 1a + b, 4, 7, 8, 9, 11, 12, 21, and 24, seemed to be effective compared to the positive control cisplatin. The cytotoxicity of compounds 6 (9.24%) for MCF7 cancer cells, 8 (5.16%) and 4 (8.26%) for HT29 cancer cells, 24 (9.84%) for Hep3B cells and 8 (8.52%), 7 (5.70%), 4 (6.94) and 9 (7.22%) for C6 cells were at normal values. And also cytotoxic activity of four compounds (5, 9, 21, and 24) among the all synthetic groups, were evaluated to the HeLa and RPE. Compound 5 showed anticancer activity on HeLa and RPE cancer cells as much as or better than cisplatin which was used as standard.

Phosphatidylinositol 3-kinase (PI3K) inhibitors: a recent update on inhibitor design and clinical trials (2016-2020)

Introduction: The phosphatidylinositol 3-kinase/protein kinase-B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway plays a central role in regulating cell growth and proliferation and thus has been considered as effective anticancer drug targets. Many PI3K inhibitors have been developed and progressed to various stages of clinical trials, and some have been approved as anticancer treatment. In this review, we discuss the drug design and clinical development of PI3K inhibitors over the past 4 years. We review the selectivity and potency of 47 PI3K inhibitors. Structural determinants for increasing selectivity toward PI3K subtype-selectivity or mutant selectivity are discussed. Future research direction and current clinical development in combination therapy of inhibitors involved in PI3Ks are also discussed.Area covered: This review covers clinical trial reports and patent literature on PI3K inhibitors and their selectivity published between 2016 and 2020.Expert opinion: To PI3Kα mutants (E542K, E545K, and H1047R), it is highly desirable to design and develop mutant-specific PI3K inhibitors. It is also necessary to develop subtype-selective PI3Kα inhibitors to minimize toxicity. To reduce drug resistance and to improve efficacy, future studies should include combination therapy of PI3K inhibitors with existing anticancer drugs from different pathways.

Docking Studies and Antiproliferative Activities of 6-(3-aryl-2-propenoyl)-2(3H)- benzoxazolone Derivatives as Novel Inhibitors of Phosphatidylinositol 3-Kinase (PI3Kα)

BACKGROUND

Cancer is a life-threatening group of diseases and universally, the second main cause of death. The design and development of new scaffolds targeting selective cancer cells are considered a promising goal for cancer treatment.

AIMS AND OBJECTIVE

Chalcone derivatives; 6-(3-aryl-2-propenoyl)-2(3H)-benzoxazolone, were previously prepared and evaluated against the oral cavity squamous cell carcinoma cell line, HSC-2, and were reported to have remarkably high tumor selectivity. The aim of this study was to further investigate the anticancer activities of the chalcone derivatives against human colon cancer cells with a possible elucidation of their mechanism of action.

METHODS

Computational studies were conducted to explore the potential interaction of the synthesized molecules with the phosphatidylinositol-4,5-bisphosphate 3-kinaseα (PI3Kα). Biological evaluation of the antiproliferative activities associated with compounds 1-23 was carried out against the colon cancer cell line, HCT116. Lactate Dehydrogenase (LDH) activity was measured to study necrosis, while the caspase-3 activation and DNA measurements were used to evaluate apoptosis in the treated cells.

RESULTS

Glide studies against PI3Kα kinase domain demonstrated that the 6-(3-aryl-2-propenoyl)-2(3H)- benzoxazolone scaffold forms H-bond with K802, Y836, E849, V851, N853, Q859, and D933, and it fits the fingerprint of PI3Kα active inhibitors. Biological evaluation of the reported compounds in HCT116 cell line confirmed that the series inhibited PI3Kα activity and induced apoptosis via activation of caspase-3 and reduction of DNA content.

CONCLUSION

The recently developed compounds might be employed as lead structures for the design of new antitumor drugs targeting PI3Kα.

N-Phenyl-6-Chloro-4-Hydroxy-2-Quinolone-3-CarboxAmides: Molecular Docking, Synthesis, and Biological Investigation as Anticancer Agents

Cancer is a multifactorial disease and the second leading cause of death worldwide. Diverse factors induce carcinogenesis, such as diet, smoking, radiation, and genetic defects. The phosphatidylinositol 3-kinase (PI3Kα) has emerged as an attractive target for anticancer drug design. Eighteen derivatives of N-phenyl-6-chloro-4-hydroxy-2-quinolone-3-carboxamide were synthesized and characterized using FT-IR, NMR (¹H and ¹³C), and high-resolution mass spectra (HRMS). The series exhibited distinct antiproliferative activity (IC₅₀ µM) against human epithelial colorectal adenocarcinoma (Caco-2) and colon carcinoma (HCT-116) cell lines, respectively: compounds 16 (37.4, 8.9 µM), 18 (50.9, 3.3 µM), 19 (17.0, 5.3 µM), and 21 (18.9, 4.9 µM). The induced-fit docking (IFD) studies against PI3Kαs showed that the derivatives occupy the PI3Kα binding site and engage with key binding residues.

Molecular Modeling, Synthesis and Biological Evaluation of N-Phenyl-4-Hydroxy-6-Methyl-2-Quinolone-3-CarboxAmides as Anticancer Agents

The emergence of phosphatidylinositol 3-kinase (PI3Kα) in cancer development has accentuated its significance as a potential target for anticancer drug design. Twenty one derivatives of N-phenyl-4-hydroxy-6-methyl-2-quinolone-3-carboxamide were synthesized and characterized using NMR (¹H and ¹³C) and HRMS. The derivatives displayed inhibitory activity against human epithelial colorectal adenocarcinoma (Caco-2) and human colon cancer (HCT-116) cell lines: compounds 8 (IC₅₀ Caco-2 = 98 µM, IC₅₀ HCT-116 = 337 µM) and 16 (IC₅₀ Caco-2 = 13 µM, IC₅₀ HCT-116 = 240.2 µM). Results showed that compound 16 significantly affected the gene encoding AKT, BAD, and PI3K. The induced-fit docking (IFD) studies against PI3Kα demonstrated that the scaffold accommodates the kinase domains and forms H-bonds with significant binding residues.

Molecular modeling, docking and dynamic simulations of growth hormone receptor (GHR) of Labeo rohita

Growth hormones (GH) have diverse functions like growth promotion, metabolism, appetite, reproduction and social behavior in vertebrates, which is mediated through the growth hormone receptor (GHR). This work was aimed to analyze structural features, homology modeling and molecular docking of Labeo rohita GHR protein. A physicochemical characteristic, like molecular weight was 67.2 kDa and hydropathicity was 0.336. Protein modeling and structure confirmation of L. rohita GHR protein showed 92.7% residues are in the favored region. Selection of ligands and molecular docking shown Melengestrol and Riboflavin ligand showed uppermost binding energy values -7.8 and -7.3 kcal/mol. Molecular interactions describe conventional hydrogen bonding of Melengestrol was observed with VAL94, GLU97, GLU95, TRP57, PHE33, THR34, PRO35, ASP36, PRO37, ARG49, GLY292, LYS291, ILE290, ALA287, LYS289 residues. Riboflavin hydrogen bonds interaction was at PRO37, ASP36, PRO35, THR34, ARG49, SER144, VAL443, GLN442, PRO284, ASP294, ILE285, PRO286, SER408, ALA287, GLY292, LYS291, ILE290, PRO288, LYS287. Molecular dynamics simulation outcomes revealed that complex 2 (Riboflavin and GHR protein) is better than complex1 (Melengestrol and GHR protein). Overall, the results of the present work lead identification of novel molecules that may be agonistic of growth hormone receptor protein and can be used to surge growth in fish. Communicated by Ramaswamy H. Sarma.

Ligand-Based Drug Design: Synthesis and Biological Evaluation of Substituted Benzoin Derivatives as Potential Antitumor Agents

Background:

Phosphoinositide 3-kinase α (PI3Kα) has emerged as a promising target for anticancer drug design.

Objectives:

Target compounds were designed to investigate the effect of the p-OCH3 motifs on ligand/PI3Kα complex interaction and antiproliferative activity.

Methods:

Synthesis of the proposed compounds, biological examination tests against human colon adenocarcinoma (HCT-116), breast adenocarcinoma (MCF-7), and breast carcinoma (T47D) cell lines, along with Glide docking studies.

Results:

A series of 1,2-bis(4-methoxyphenyl)-2-oxoethyl benzoates was synthesized and characterized by means of FT-IR, 1H and 13C NMR, and by elemental analysis. Biological investigation demonstrated that the newly synthesized compounds exhibit antiproliferative activity in human colon adenocarcinoma (HCT-116), breast adenocarcinoma (MCF-7), and breast carcinoma (T47D) cell lines possibly via inhibition of PI3Kα and estrogen receptor alpha (ERα). Additionally, results revealed that these compounds exert selective inhibitory activity, induce apoptosis, and suppress VEGF production. Compound 3c exhibited promising antiproliferative activity in HCT-116 interrogating that hydrogen bond-acceptor mediates ligand/PI3Kα complex formation on m- position. Compounds 3e and 3i displayed high inhibitory activity in MCF-7 and T47D implying a wide cleft discloses the o-attachment. Furthermore, compound 3g exerted selective inhibitory activity against T47D. Glide docking studies against PI3Kα and ERα demonstrated that the series accommodate binding to PI3Kα and/or ERα.

Conclusion:

The series exhibited a potential antitumor activity in human carcinoma cell lines encoding PI3Kα and/or ERα.

DPP-IV Inhibitory Phenanthridines: Ligand, Structure-Based Design and Synthesis

BACKGROUND

Lately, diabetes has become the main health concern for millions of people around the world. Dipeptidyl peptidase-IV (DPP-IV) inhibitors have emerged as a new class of oral antidiabetic agents. Formerly, acridines, N4-sulfonamido-succinamic, phthalamic, acrylic and benzoyl acetic acid derivatives, and sulfamoyl-phenyl acid esters were designed and developed as new DPP-IV inhibitors.

OBJECTIVE

This study aims to develop a pharmacophore model of DPP-IV inhibitors and to evaluate phenanthridines as a novel scaffold for inhibiting DPP-IV enzyme. In addition, to assess their binding interactions with the enzyme through docking in the binding site of 4A5S (PDB).

METHODS

Herein, Quantum-Polarized Ligand Docking (QPLD) and ligand-based pharmacophore modeling investigations were performed. Three novel 3,8-disubstituted-6-phenyl phenanthridine derivatives 3-5 have been designed, synthesized and characterized. In vitro biological testing against DPP-IV was carried out using fluorometric assay kit.

RESULTS

QPLD study demonstrates that compounds 3-5 forms H-bond with Lys554, Trp629, and Tyr631, besides charge transfer interaction between their aromatic rings and the aromatic rings of Tyr547 and Tyr666. Moreover, they fit the three pharmacophoric point features of DPP-IV inhibitors and were proven to have in vitro DPP-IV inhibitory activity where compound 5 displayed a % inhibition of 45.4 at 100 μM concentration.

CONCLUSION

Phenanthridines may serve as a potential lead compound for developing new DPP-IV inhibitors as a promising antidiabetic agent. Computational results suggest future structural simplification.

Synthesis, characterization, and anticancer evaluation of some new N1-(anthraquinon-2-yl) amidrazone derivatives

A new series of novel N1-anthraquinon-2-yl amidrazones incorporating N-piperazines and related congeners were synthesized via reaction of the hydrazonoyl chloride derived from 2-qaminoanthraquinone with the appropriate piperazine (secondary amine). Structures of the new compounds were confirmed by a panel of spectroscopic methods including IR, NMR, and MS and by elemental analysis. The antitumor activity of the newly prepared compounds was evaluated in vitro against MCF-7 breast cancer, K562 chronic myelogenous leukemia, and dermal fibroblasts cell lines by means of a cell viability assay using the tetrazolium dye 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide. Results revealed that compounds 13a and 13d exhibit the highest inhibitory activity against K562 and MCF-7 cell lines. These two compounds could be considered as promising as potential anticancer drugs.

Novel amphiphilic pyridinium ionic liquids-supported Schiff bases: ultrasound assisted synthesis, molecular docking and anticancer evaluation

Background

Pyridinium Schiff bases and ionic liquids have attracted increasing interest in medicinal chemistry.

Results

A library of 32 cationic fluorinated pyridinium hydrazone-based amphiphiles tethering fluorinated counteranions was synthesized by alkylation of 4-fluoropyridine hydrazone with various long alkyl iodide exploiting lead quaternization and metathesis strategies. All compounds were assessed for their anticancer inhibition activity towards different cancer cell lines and the results revealed that increasing the length of the hydrophobic chain of the synthesized analogues appears to significantly enhance their anticancer activities. Substantial increase in caspase-3 activity was demonstrated upon treatment with the most potent compounds, namely 8, 28, 29 and 32 suggesting an apoptotic cellular death pathway.

Conclusions

Quantum-polarized ligand docking studies against phosphoinositide 3-kinase α displayed that compounds 2–6 bind to the kinase site and form H-bond with S774, K802, H917 and D933.

Electronic supplementary material

The online version of this article (10.1186/s13065-018-0489-z) contains supplementary material, which is available to authorized users.

Facile synthesis, characterization, and cytotoxicity study of new 3-(indol-2-yl)bicyclotetrazatridecahexaens

A new series of thiosemicarbazone-based indole derivatives 12–15 has been prepared by condensation reaction of indole-2-carboxamide derivatives 8–11 with thiosemicarbazide. The former compounds underwent intracyclization in the presence of chloroacetic acid and sodium acetate to afford a set of new 3-(indol-2-yl)bicyclotetrazatridecahexaens 16–19. These newly synthesized compounds have been characterized by means of FTIR, 1H NMR, 13C NMR, and HRMS and by elemental analyses. Cytotoxic activities of the prepared compounds along with LY294002 were evaluated in vitro against normal human skin fibroblast, human colon carcinoma (HCT116), and leukemia (K562) cell lines; results revealed that the series inhibits only HCT116 cell line. In addition, results showed that compound 18 exerts moderate potency in HCT116 with an IC50 value of 54 μmol/L and significantly induces apoptosis.

Molecular docking as a popular tool in drug design, an in silico travel

New molecular modeling approaches, driven by rapidly improving computational platforms, have allowed many success stories for the use of computer-assisted drug design in the discovery of new mechanism-or structure-based drugs. In this overview, we highlight three aspects of the use of molecular docking. First, we discuss the combination of molecular and quantum mechanics to investigate an unusual enzymatic mechanism of a flavoprotein. Second, we present recent advances in anti-infectious agents' synthesis driven by structural insights. At the end, we focus on larger biological complexes made by protein-protein interactions and discuss their relevance in drug design. This review provides information on how these large systems, even in the presence of the solvent, can be investigated with the outlook of drug discovery.

Computer-aided design, synthesis, and biological evaluation of new indole-2-carboxamide derivatives as PI3Kα/EGFR inhibitors

Structure-based drug design and molecular modeling were employed to identify a new series of indole-2-carboxamides as potential anticancer agents. These compounds were synthesized and characterized with the aid of several spectroscopic techniques, such as FT-IR, NMR, and mass spectrometry as well as by elemental analysis. Molecular docking studies confirmed that the newly synthesized compounds accommodate PI3Kα and EGFR kinase catalytic sites and form H-bonding with the key binding residues. The antitumor activity of these new compounds against an array of cancer cell lines (human colon carcinoma (HCT116), leukemia (K562), and breast cancer (MDA231) was evaluated. Results revealed that these compounds were selective against the kinase domain, and none of them showed any inhibitory activity against K562. In addition, results showed that compound 13 exhibited high potency in HCT116 and MDA231 with IC50 values of 19 and 15μM, respectively. Our findings recommend that further optimization of this series would be beneficial for colon and breast cancer treatment.